| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-02-15 | Filter out files that only have "None". | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-14 | Capitalize the first string of every path. | Munyoki Kilyungi | |
| This is done to match the RDF identifier. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Convert extra dataset metadata to text-files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Remove more fields from dataset's RDF output. | Munyoki Kilyungi | |
| These are: "Experiment_Type", "Contributors" & "Citation" which are already in RTF form. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-13 | Fix missplaced parens. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-09 | Re-add triplets that describe dataset terms. | Munyoki Kilyungi | |
| These triplets will be re-used when constructing the json-ld endpoints for GN3. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-09 | Update push and reset git commands. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-09 | Use correct path to the datasets directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Delete rdf triplets from dataset transform. | Munyoki Kilyungi | |
| These triplets are now stored as text files and versioned in git. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Add method for commiting changes to the gn-docs git repo. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Delete unused variable in the getopts arglist. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Fix typo. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Fix how the dataset directory is constructed. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Remove "string->identifier" for the dataset directory name. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Use correct format string literal when printing out sql results. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Update local git-repo directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-02-08 | Add a basic guile script to transform stored rtf data to files. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-08 | Add InfoFiles.Experiment_Type metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-01-05 | Correct formatting for the gnt:location predicate for ProbeSets. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Fix typo with pantherLink ResourceLink. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use correct property for classifying pantherLink as a resource. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Delete duplicate entries for gnc:biogpsLink/gnc:gtexLink. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Update handling of RGD_ID field in genelist metadata transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Replace gnt:symbol with gnt:geneSymbol. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Refactor gene metadata RDF transform. | Munyoki Kilyungi | |
| In the case of the GeneList_rn33 table, the table id is used, since there is no other way to uniquely identify a gene using the other fields. See the following for more details: https://issues.genenetwork.org/issues/transform-genelist-to-rdf Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Replace gnc:GeneSymbol with gnc:Gene. | Munyoki Kilyungi | |
| A GeneSymbol != Gene. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Delete "GROUP BY" when transforming genelist/genelist_rn33 metadata. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use gnt:geneSymbol instead of rdfs:label/gnt:symbol. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Use gnt:hasGeneId instead of gnt:gene/dct:references. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-22 | Move gnt:hasGeneId definitions to genelist.scm | Munyoki Kilyungi | |
| * examples/generif.scm: Move definitions for gnt:hasGeneId from here to... * examples/genelist.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-20 | Set up as Guix channel for CI. | Arun Isaac | |
| * .guix-channel, .guix/gn-transform-databases-package.scm, guix.scm: New files. | |||
| 2023-12-20 | Use guile to run tests. | Arun Isaac | |
| Disuse run64. * Makefile (RUN64): Delete variable. (GUILE): New variable. (check): Use GUILE to run tests. | |||
| 2023-12-20 | Set correct top level module directory. | Arun Isaac | |
| 2023-12-20 | Fix srfi-26 import typo. | Arun Isaac | |
| 2023-12-15 | Preserve gene symbol case when used as an identifer. | Munyoki Kilyungi | |
| Genes with varying casing (e.g., Shh, SHH) result in `string->identifier` capitalizing the first letter by default. This creates inconsistencies in gene symbols, leading to different predicates and objects for the same entity, introducing errors. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Use URI encoding for OMIM and homologene resource link handling. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Refactor Uniprot and GeneId handling in ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Add missing "gene:" prefix in ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Trim gene symbol rdfs:label for the GeneList_rn33 table. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-15 | Use URI encoding for symbol-based resource link URLs. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Remove "remap-species-identifiers" from generif transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Link extra resources to genes and trim gene symbols. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Refactor symbol identifier in strains.scm. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Add GeneList metadata RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Remove some resource links from ProbeSet RDF transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-14 | Use correct identifier for the AvgMethod table. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiedUnder -> gnt:belongsToGroup. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiedUnder -> gnt:belongsToSpecies for species. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Replace xkos:classifiendUnder with gnt:belongsToGroup for groups. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-12-04 | Fix typo in publishfreeze transform. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
 |
index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
| aboutsummaryrefslogtreecommitdiff |